Variant report

Variant	rs11707938
Chromosome Location	chr3:52319215-52319216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr3:52319206-52319751	HepG2	liver:	n/a	n/a
2	EP300	chr3:52319206-52319675	HepG2	liver:	n/a	n/a
3	HEY1	chr3:52319130-52319648	HepG2	liver:	n/a	n/a
4	ARID3A	chr3:52319176-52319727	HepG2	liver:	n/a	n/a
5	TEAD4	chr3:52319165-52319764	HepG2	liver:	n/a	n/a
6	ZNF384	chr3:52319152-52319583	GM12878	blood:	n/a	n/a
7	GATA3	chr3:52319177-52319821	A549	lung:	n/a	n/a
8	MYBL2	chr3:52319083-52319836	HepG2	liver:	n/a	n/a
9	FOXA1	chr3:52319195-52319784	HepG2	liver:	n/a	n/a
10	SP1	chr3:52319159-52319776	HepG2	liver:	n/a	n/a
11	ELF1	chr3:52319155-52319577	HepG2	liver:	n/a	n/a
12	FOXA2	chr3:52319141-52319917	HepG2	liver:	n/a	n/a
13	TCF12	chr3:52319085-52319811	A549	lung:	n/a	n/a
14	SP1	chr3:52319195-52319739	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52272181..52276088-chr3:52318615..52323958,11	MCF-7	breast:
2	chr3:52304087..52306795-chr3:52318600..52320906,2	K562	blood:
3	chr3:52311051..52315983-chr3:52317623..52323290,10	MCF-7	breast:
4	chr3:52269288..52271694-chr3:52319110..52321005,2	MCF-7	breast:
5	chr3:52318594..52322784-chr3:52322985..52327026,4	MCF-7	breast:
6	chr3:52317125..52319496-chr3:52319751..52323578,5	K562	blood:

No data

Variant related genes	Relation type
GLYCTK	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000168237	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11720866	0.91[EUR][1000 genomes]
rs56296139	0.97[EUR][1000 genomes]
rs73088787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088790	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52313200-52321000	Weak transcription	Gastric	stomach
2	chr3:52313400-52320400	Weak transcription	Lung	lung
3	chr3:52313400-52321000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52313600-52320800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:52313600-52320800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:52313600-52320800	Weak transcription	Colonic Mucosa	Colon
7	chr3:52313600-52321000	Enhancers	Fetal Intestine Large	intestine
8	chr3:52313600-52321000	Weak transcription	Left Ventricle	heart
9	chr3:52313600-52321000	Weak transcription	Psoas Muscle	Psoas
10	chr3:52313600-52321000	Weak transcription	Right Atrium	heart
11	chr3:52313800-52320800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:52313800-52320800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:52314000-52320800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:52314000-52320800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:52314000-52321000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:52314200-52320800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:52314200-52320800	Weak transcription	Fetal Brain Female	brain
18	chr3:52314200-52320800	Weak transcription	NHLF	lung
19	chr3:52314400-52320400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:52314400-52320600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:52314400-52320600	Weak transcription	Dnd41	blood
22	chr3:52314400-52320800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:52314400-52320800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:52314400-52320800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:52314400-52320800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:52314400-52320800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:52314400-52320800	Weak transcription	Brain Substantia Nigra	brain
28	chr3:52314400-52320800	Weak transcription	HMEC	breast
29	chr3:52314400-52320800	Weak transcription	NHEK	skin
30	chr3:52314400-52321000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:52314600-52320600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:52314600-52320800	Weak transcription	Brain Anterior Caudate	brain
33	chr3:52314600-52320800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:52314600-52320800	Weak transcription	Fetal Lung	lung
35	chr3:52314600-52321000	Weak transcription	Brain Germinal Matrix	brain
36	chr3:52314800-52320400	Weak transcription	Pancreas	Pancrea
37	chr3:52314800-52320400	Weak transcription	HSMM	muscle
38	chr3:52314800-52320600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:52314800-52320800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:52314800-52320800	Weak transcription	Brain Angular Gyrus	brain
41	chr3:52314800-52320800	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:52314800-52320800	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:52314800-52320800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:52314800-52320800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:52314800-52321000	Weak transcription	Right Ventricle	heart
46	chr3:52315800-52320400	Enhancers	Liver	Liver
47	chr3:52315800-52320400	Enhancers	HepG2	liver
48	chr3:52315800-52320800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:52316400-52319400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr3:52316400-52320600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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